We obtained genome-wide transcription factor binding data in mouse ES cells from 2 sources. The transcription factors Oct4, Sox2, Nanog, and Tcf3 were downloaded from the Gene Expression Omnibus (GSE11724) and the cMyc, nMyc, Zfx, Stat3, Smad1, Klf4, and Esrrb from GEO (GSE11431). For each ChIP-Seq dataset, the raw reads were obtained from the SRA (http://www.ncbi.nlm.nih.gov/sra) and processed as follows. (i) The reads were all aligned to the mouse genome assembly (build MM9) using the Bowtie aligner66, requiring a single best placement of each read. All reads with multiple acceptable placements were removed from the analysis. (ii) Binding sites were determined from the aligned reads using the MACS67 (http://liulab.dfci.harvard.edu/MACS/) algorithm using the default parameters with –mfold 8 to account for varying read counts in the libraries. (iii) lincRNA promoter regions were defined as previously described2,3 using the location of the K4me3 peaks overlapping or within 5Kb of the transcriptional start site determined by RNA-Seq reconstruction. (iv) The transcription factor binding locations and lincRNA promoter locations were intersected and the enrichment level of the peak overlapping a lincRNA promoter was assigned
